Merge branch 'containerized_vizapp' into 'master'

Fix to defaults so that singularity is in the biohpc.config as the default,...

Closes #1

See merge request biohpc/astrocyte_example_wordcount!4

.gitlab-ci.yml

@@ -133,8 +133,6 @@ cache_docker_image:
 singularity_astrocyte_test:
   stage: test_singularity
   script:
-  # Note the biohpc_singularity.config replacement.
-  - sed -i 's|nextflow_config\x3A \x27biohpc.config\x27|nextflow_config\x3A \x27biohpc_singularity.config\x27|' astrocyte_pkg.yml
   - astrocyte_cli run "$CI_PROJECT_DIR" --option=q
   - test -s "$CI_PROJECT_DIR/workflow/output/mobydick.txt.uppercase.tolines.wordcount"
 
@@ -181,5 +179,6 @@ astrocyte_shiny:
   - sleep 5
   - unset http_proxy
   - unset all_proxy
+  - unset https_proxy
   - wget "http://127.0.0.1:8123"
 

README.md

@@ -20,6 +20,10 @@ The workflow `workflow/main.nf` has three processes:
 There is a single parameter `story`. This provides 1 or more files that the
 workflow should run on.
 
+## Containers
+
+The default configuration for this workflow is located in ./workflow/configs/biohpc.config . This configuration will cause the Nextflow command to use the singularity executor for the uppercase, toLines, and wordcount processes, using Docker.io endpoints. The biohpc_*_gitlab.config files show how to instead use images pulled from a specified GitLab repository.
+
 ## Questions
 
 If you have any questions about this workflow example, or Astrocyte in general,

astrocyte_pkg.yml

@@ -171,14 +171,13 @@ workflow_parameters:
 #            The workflow must publish all final output into $baseDir
 
 # Name of the R module that the vizapp will run against
-vizapp_r_module: 'R/3.4.1-gccmkl'
+vizapp_r_module: 'R/3.6.1-gccmkl'
 
 # List of any CRAN packages, not provided by the modules, that must be made
 # available to the vizapp
 vizapp_cran_packages:
-  - shiny
-  - shinyFiles
-
+  - plotly 
+    
 # # List of any Bioconductor packages, not provided by the modules, that must be made
 # available to the vizapp
 vizapp_bioc_packages:

vizapp/server.R

@@ -10,12 +10,41 @@ rootdir <- Sys.getenv('outputDir')
 
 
 shinyServer(function(input, output, session) {
+shinyFileChoose(input, 'files', roots=c('output'=rootdir), session=session)
+  ## print to console to see how the value of the shinyFiles
+  ## button changes after clicking and selection
 
-    # The backend for a simple file chooser, restricted to the
-    # rootdir we obtained above.
-    # See https://github.com/thomasp85/shinyFiles
+  observe({
 
-    shinyFileChoose(input, 'files', roots=c('output'=rootdir), filetypes=c(''
-                                                                             ,'txt'), session=session)
+    if (is.integer(input$files)) {
+      cat("No files have been selected (shinyFileChoose)")
+    } else {
+      cat("\ninput$files value:\n\n")
+      print(input$files)
+      files <- parseFilePaths(c('output'=rootdir), input$files)
+      print(files)
+
+      wordcounts <- read.table(files$datapath[1], quote="\"", comment.char="")
+
+      colnames(wordcounts) <- c("count","word");
+      wordcounts_total <- sum(wordcounts$count);
+      wordcounts$freq <- wordcounts$count / wordcounts_total;
+
+      wordcounts <- wordcounts[,c("word", "count", "freq")];
+      wordcounts$rank = order(wordcounts$count)
+
+      wordcounts <- wordcounts[wordcounts$count>3,]
+      wordcounts_total <- sum(wordcounts$count);
+      wordcounts$freq <- wordcounts$count / wordcounts_total;
+
+
+      output$table <- renderDataTable(wordcounts)
+
+
+      output$plot <- renderPlotly(
+        plot1 <- plot_ly(x = wordcounts$rank, y = wordcounts$freq)
+      )
+    }
+  })
 
 })

vizapp/ui.R

 library(shiny)
 library(shinyFiles)
-
+library(plotly)
 
 shinyUI(fluidPage(
 
   verticalLayout(
 
-    # Application title
-    titlePanel("Astrocyte Example"),
 
-    wellPanel(
+  # Application title
+  titlePanel("Astrocyte Example"),
+
+  wellPanel(
 
-        helpText("This is a minimal example, demonstrating how
-        a Shiny visualization application can access the output of a workflow.
-        Here we provide a file browser using the shinyFiles package. Real
-        Astrocyte vizapps would provide custom methods to access and visualize
-        output."),
+    helpText("This is a minimal example, demonstrating how
+             a Shiny visualization application can access the output of a workflow.
+             Here we provide a file browser using the shinyFiles package. Real
+             Astrocyte vizapps would provide custom methods to access and visualize
+             output."),
 
         helpText("The workflow output is in the directory set in the
-        outputDir environment variable. this can be retrieved in R with the
-        command Sys.getenv('outputDir')"),
+                 outputDir environment variable. this can be retrieved in R with the
+                 command Sys.getenv('outputDir')"),
 
         # A simple file browser within the workflow output directory
         # See https://github.com/thomasp85/shinyFiles
         shinyFilesButton('files', label='Browse workflow output', title='Please select a file', multiple=FALSE)
 
-    )
+    ),
+    plotlyOutput('plot'),
+    dataTableOutput('table')
+
+
   )
-))
\ No newline at end of file
+))

workflow/configs/biohpc.config

@@ -6,4 +6,13 @@ singularity {
 
 process {
     executor = 'local'
+    withName:uppercase {
+        container = 'ubuntu:latest'
+    }
+    withName:tolines {
+        container = 'ubuntu:latest'
+    }
+    withName:wordcounts {
+        container = 'centos:centos8'
+    }
 }

workflow/configs/biohpc_docker_gitlab.config

@@ -7,12 +7,12 @@ docker {
 process {
     executor = 'local'
     withName:uppercase {
-        container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
+        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:tolines {
-        container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
+        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:wordcounts {
-        container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/centos:centos8'
+        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
     }
 }

workflow/configs/biohpc_singularity.config

-singularity {
-  enabled = true
-  runOptions = '--bind /vagrant:/vagrant'
-  cacheDir = "$baseDir/images/singularity"
-}
-
-process {
-    executor = 'local'
-    withName:uppercase {
-        container = 'ubuntu:latest'
-    }
-    withName:tolines {
-        container = 'ubuntu:latest'
-    }
-    withName:wordcounts {
-        container = 'centos:centos8'
-    }
-}

workflow/configs/biohpc_singularity_gitlab.config

@@ -8,15 +8,15 @@ singularity {
 process {
     executor = 'local'
     withName:parameters {
-        container = 'git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
+        container = 'git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:uppercase {
-        container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
+        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:tolines {
-        container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/ubuntu:latest'
+        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/ubuntu:latest'
     }
     withName:wordcounts {
-        container = 'docker://git.biohpc.swmed.edu:5050/s190450/astrocyte_example_wordcount/centos:centos8'
+        container = 'docker://git.biohpc.swmed.edu:5050/biohpc/astrocyte_example_wordcount/centos:centos8'
     }
 }